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(-) Description

Title :  CRYSTAL STRUCTURE OF CBPF IN COMPLEX WITH IPRATROPIUM BY SOAKING
 
Authors :  N. Silva-Martin, J. A. Hermoso
Date :  10 Mar 10  (Deposition) - 06 Apr 11  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Choline-Binding-Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. S. Martin, M. G. Retamosa, B. Maestro, S. G. Bartual, M. J. Rodes, P. Garcia, J. M. Sanz, J. A. Hermoso
Crystal Structures Of Cbpf Complexed With Atropine And Ipratropium Reveal Clues For The Design Of Novel Antimicrobials Against Streptococcus Pneumoniae.
Biochim. Biophys. Acta V. 1840 129 2013
PubMed-ID: 24036328  |  Reference-DOI: 10.1016/J.BBAGEN.2013.09.006

(-) Compounds

Molecule 1 - CHOLINE-BINDING PROTEIN F
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIN-III-A3
    Expression System Taxid: 562
    Fragment: RESIDUES 28-338
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CHT6Ligand/IonCHOLINE ION
2GOL6Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4X8M3Ligand/IonIPRATROPIUM

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:244 , ARG A:246 , SER A:247 , HOH A:2392BINDING SITE FOR RESIDUE SO4 A1312
02AC2SOFTWARETYR A:203 , GLY A:205 , SER A:206 , SER A:207 , LYS A:215 , GOL A:1317 , HOH A:2393BINDING SITE FOR RESIDUE GOL A1313
03AC3SOFTWARETRP A:163 , TRP A:181 , ASN A:198 , MET A:210 , LYS A:227 , ASN A:228 , HOH A:2242 , HOH A:2266 , HOH A:2288 , HOH A:2312 , HOH A:2394BINDING SITE FOR RESIDUE X8M A1314
04AC4SOFTWARETYR A:56 , ASN A:67 , ASP A:121 , ASN A:122 , HOH A:2109 , HOH A:2112BINDING SITE FOR RESIDUE GOL A1315
05AC5SOFTWARETRP A:276 , TRP A:283 , TYR A:301 , TRP A:309BINDING SITE FOR RESIDUE X8M A1316
06AC6SOFTWAREPHE A:204 , GLY A:205 , SER A:207 , SER A:209 , ALA A:211 , LYS A:215 , GOL A:1313 , HOH A:2290 , HOH A:2295BINDING SITE FOR RESIDUE GOL A1317
07AC7SOFTWAREPHE A:7 , LYS A:14 , ILE A:29 , ASP A:30 , LYS A:32 , TYR A:34 , MET A:42 , ASP A:81 , TYR A:287 , HOH A:2169BINDING SITE FOR RESIDUE X8M A1318
08AC8SOFTWAREASP A:149 , TRP A:221 , HOH A:2396 , HOH A:2397BINDING SITE FOR RESIDUE GOL A1319
09AC9SOFTWARETYR A:48 , GLN A:72 , GLU A:73 , LYS A:142 , TYR A:151 , ILE A:156 , THR A:170 , HOH A:2252 , HOH A:2398 , HOH A:2399BINDING SITE FOR RESIDUE GOL A1320
10BC1SOFTWARELYS A:196 , GLN A:257 , TRP A:262 , TYR A:305 , ASN A:306BINDING SITE FOR RESIDUE GOL A1321
11BC2SOFTWARETRP A:194 , MET A:231 , SER A:248 , HOH A:2306BINDING SITE FOR RESIDUE CHT A1322
12BC3SOFTWARETRP A:255 , TRP A:262 , LEU A:292 , ASN A:306BINDING SITE FOR RESIDUE CHT A1323
13BC4SOFTWARETRP A:214 , MET A:251 , GLY A:268 , ASN A:269 , HOH A:2402BINDING SITE FOR RESIDUE CHT A1324
14BC5SOFTWARETRP A:235 , TRP A:242 , TYR A:263 , SER A:289BINDING SITE FOR RESIDUE CHT A1325
15BC6SOFTWARETRP A:137 , TYR A:182 , MET A:190 , SER A:207BINDING SITE FOR RESIDUE CHT A1326
16BC7SOFTWARETYR A:119 , GLU A:133 , TYR A:138 , HOH A:2213BINDING SITE FOR RESIDUE CHT A1327

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X8M)

(-) Exons   (0, 0)

(no "Exon" information available for 2X8M)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:311
 aligned with Q8DR52_STRR6 | Q8DR52 from UniProtKB/TrEMBL  Length:338

    Alignment length:311
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         Q8DR52_STRR6    28 NTTGGRFVDKDNRKYYVKDDHKAIYWHKIDGKTYYFGDIGEMVVGWQYLEIPGTGYRDNLFDNQPVNEIGLQEKWYYFGQDGALLEQTDKQVLEAKTSENTGKVYGEQYPLSAEKRTYYFDNNYAVKTGWIYEDGNWYYLNKLGNFGDDSYNPLPIGEVAKGWTQDFHVTIDIDRSKPAPWYYLDASGKMLTDWQKVNGKWYYFGSSGSMATGWKYVRGKWYYLDNKNGDMKTGWQYLGNKWYYLRSSGAMVTGWYQDGLTWYYLNAGNGDMKTGWFQVNGKWYYAYSSGALAVNTTVDGYSVNYNGEWVQ 338
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (8)
           Pfam domains (9) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8mA0------------------- Pfam domains (9)
         Sec.struct. author ....eeeeee..eeeeee..eeee.eeee..eeee.........eeeeee.........ee...........eeeeee...........eeeee....................eeeee.........eeeee..eeeee....eee..eee.........eeee...............eeee.........eeee..eeee.........eeeee..eeeee.........eeeee..eeeee........eeeee..eeeee.........eeeee..eeeee.........ee....ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8m A   1 NTTGGRFVDKDNRKYYVKDDHKAIYWHKIDGKTYYFGDIGEMVVGWQYLEIPGTGYRDNLFDNQPVNEIGLQEKWYYFGQDGALLEQTDKQVLEAKTSENTGKVYGEQYPLSAEKRTYYFDNNYAVKTGWIYEDGNWYYLNKLGNFGDDSYNPLPIGEVAKGWTQDFHVTIDIDRSKPAPWYYLDASGKMLTDWQKVNGKWYYFGSSGSMATGWKYVRGKWYYLDNKNGDMKTGWQYLGNKWYYLRSSGAMVTGWYQDGLTWYYLNAGNGDMKTGWFQVNGKWYYAYSSGALAVNTTVDGYSVNYNGEWVQ 311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2X8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X8M)

(-) Pfam Domains  (1, 9)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CW_binding_1] (12)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2X8M)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8DR52_STRR6 | Q8DR52: 2v04 2v05 2vyu 2x8o 2x8p

(-) Related Entries Specified in the PDB File

2v04 CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE
2v05 CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE. CRYSTAL FORM II.
2vyu CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE IN THE PRESENCE OF A PEPTIDOGLYCAN ANALOGUE (TETRASACCHARIDE-PENTAPEPTIDE)
2x8o CRYSTAL STRUCTURE OF CBPF IN COMPLEX WITH ATROPINE BY SOAKING
2x8p CRYSTAL STRUCTURE OF CBPF IN COMPLEX WITH ATROPINE BY CO-CRYSTALLIZATION